- Python 2.7
- Libraries: Biopython 1.69, matplotlib 2.0.2.
For simplicity, use Anaconda to install required libraries.
These scripts here are working with several file formats:
- Protein Data Bank (PDB) file format: provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies. Proteins of interest can be downloaded at RCSB PDB.
- probe file format: is generated by Probe software
- Simple interaction format (SIF) file format: is used for building a graph from a list of interactions. Lines in SIF file specify a source node, a relationship type (or edge type), and one or more target nodes. (Reference: SIF file format - Cytoscape wiki)